-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_10377647-10580413

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for CodingQuarry_transcript_32720-T1
Valid prediction for GlimmerHMM_glimmerT_48516-T1
Valid prediction for snap_scaffold_21-snap.2264-T1
Valid prediction for Augustus_model.g32419.t1
Valid prediction for GlimmerHMM_glimmerT_48517-T1
Valid prediction for Augustus_model.g32413.t1
Valid prediction for snap_scaffold_21-snap.2272-T1
Valid prediction for snap_scaffold_21-snap.2275-T1
Valid prediction for snap_scaffold_21-snap.2283-T1
Couldn't classify 112125, 112178
Sorry, prediction pasa_asmbl_28877.p1 fails validation.
(ATG)	 TC	110827-110917	GT	AGG
(AGC)	 AG	111049-111168	GT	CGG
(GTT)	 AG	111287-111390	GT	AGG
(GAG)	 AG	111700-111801	GT	CGG
(AAA)	 AG	111910-111951	GT	TGG
(GAA)	 AG	112125-112178	AA	GAA
-recovered pasa_asmbl_28877.p1, initial, 110827, 110917
-recovered pasa_asmbl_28877.p1, internal, 111049, 111168
-recovered pasa_asmbl_28877.p1, internal, 111287, 111390
-recovered pasa_asmbl_28877.p1, internal, 111700, 111801
-recovered pasa_asmbl_28877.p1, internal, 111910, 111951
Valid prediction for GlimmerHMM_glimmerT_48509-T1
Valid prediction for CodingQuarry_transcript_32724-T1
Valid prediction for snap_scaffold_21-snap.2269-T1
Valid prediction for Augustus_model.g32428.t1
Valid prediction for pasa_asmbl_28881.p1
Valid prediction for Augustus_model.g32417.t1
Valid prediction for Augustus_model.g32424.t1
Valid prediction for CodingQuarry_transcript_32718-T1
Valid prediction for HiQ_model.g32423.t1
Valid prediction for Augustus_model.g32409.t1
Valid prediction for Augustus_model.g32411.t1
Couldn't classify 93505, 93627
Sorry, prediction pasa_asmbl_28876.p1 fails validation.
(TGT)	 TG	93505-93627	GT	AGG
(AAA)	 AG	94318-94386	GT	AGG
(GCT)	 AG	95115-95357	GT	AGG
(AGT)	 AG	95656-96159	GT	AGG
(ACA)	 AG	96351-96365	AG	GAA
-recovered pasa_asmbl_28876.p1, terminal, 96351, 96365
-recovered pasa_asmbl_28876.p1, internal, 94318, 94386
-recovered pasa_asmbl_28876.p1, internal, 95115, 95357
-recovered pasa_asmbl_28876.p1, internal, 95656, 96159
Valid prediction for GlimmerHMM_glimmerT_48515-T1
Valid prediction for snap_scaffold_21-snap.2301-T1
Valid prediction for Augustus_model.g32414.t1
Valid prediction for Augustus_model.g32415.t1
Valid prediction for CodingQuarry_transcript_32725-T1
Valid prediction for CodingQuarry_transcript_32722-T1
Valid prediction for GlimmerHMM_glimmerT_48521-T1
Valid prediction for snap_scaffold_21-snap.2262-T1
Valid prediction for GlimmerHMM_glimmerT_48528-T1
Valid prediction for GlimmerHMM_glimmerT_48532-T1
Valid prediction for GlimmerHMM_glimmerT_48513-T1
Valid prediction for GlimmerHMM_glimmerT_48523-T1
Valid prediction for snap_scaffold_21-snap.2285-T1
Valid prediction for snap_scaffold_21-snap.2295-T1
Valid prediction for pasa_asmbl_28880.p1
Valid prediction for GlimmerHMM_glimmerT_48531-T1
Valid prediction for snap_scaffold_21-snap.2297-T1
Valid prediction for snap_scaffold_21-snap.2274-T1
Valid prediction for snap_scaffold_21-snap.2303-T1
Valid prediction for GlimmerHMM_glimmerT_48508-T1
Valid prediction for snap_scaffold_21-snap.2292-T1
Valid prediction for snap_scaffold_21-snap.2271-T1
Valid prediction for HiQ_model.g32425.t1
Valid prediction for GlimmerHMM_glimmerT_48529-T1
Valid prediction for pasa_asmbl_28868.p1
Valid prediction for GlimmerHMM_glimmerT_48534-T1
Valid prediction for HiQ_model.g32406.t1
Valid prediction for snap_scaffold_21-snap.2267-T1
Valid prediction for GlimmerHMM_glimmerT_48520-T1
Valid prediction for snap_scaffold_21-snap.2279-T1
Valid prediction for snap_scaffold_21-snap.2299-T1
Valid prediction for GlimmerHMM_glimmerT_48518-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_21-snap.2280-T1
Valid prediction for GlimmerHMM_glimmerT_48514-T1
Valid prediction for snap_scaffold_21-snap.2270-T1
Couldn't classify 94639, 94648
Couldn't classify 96047, 96103
Sorry, prediction pasa_asmbl_28045.p1 fails validation.
(GAC)	 AA	94639-94648	GT	AGG
(ACG)	 AG	94950-95053	GT	TGG
(GGC)	 AG	95268-95388	GT	GGG
(GGG)	 AG	95586-95725	GT	TGG
(CCC)	 AG	96047-96103	CT	GCC
-recovered pasa_asmbl_28045.p1, internal, 94950, 95053
-recovered pasa_asmbl_28045.p1, internal, 95268, 95388
-recovered pasa_asmbl_28045.p1, internal, 95586, 95725
Valid prediction for HiQ_model.g32412.t1
Valid prediction for Augustus_model.g32407.t1
Valid prediction for GlimmerHMM_glimmerT_48533-T1
Valid prediction for Augustus_model.g32410.t1
Valid prediction for snap_scaffold_21-snap.2300-T1
Valid prediction for snap_scaffold_21-snap.2277-T1
Valid prediction for snap_scaffold_21-snap.2268-T1
Valid prediction for snap_scaffold_21-snap.2284-T1
Valid prediction for GlimmerHMM_glimmerT_48525-T1
Valid prediction for GlimmerHMM_glimmerT_48526-T1
Couldn't classify 67370, 67456
Sorry, prediction pasa_asmbl_28058.p1 fails validation.
(GAG)	 AC	67370-67456	GT	AGG
(GGG)	 AG	67537-67650	GT	AGG
(AAT)	 AG	67743-67838	GT	TGG
(TGG)	 AG	68532-68660	GT	CCG
(CTG)	 AG	68819-68872	AT	AAA
-recovered pasa_asmbl_28058.p1, terminal, 68819, 68872
-recovered pasa_asmbl_28058.p1, internal, 67537, 67650
-recovered pasa_asmbl_28058.p1, internal, 67743, 67838
-recovered pasa_asmbl_28058.p1, internal, 68532, 68660
Valid prediction for snap_scaffold_21-snap.2288-T1
Couldn't classify 193764, 194040
Couldn't classify 194071, 194104
Sorry, prediction CodingQuarry_transcript_32719-T1 fails validation.
(ATG)	 GT	189692-189906	GT	AGG
(GCT)	 AG	190193-190387	GT	AGG
(AAT)	 AG	190570-190688	GT	AGG
(GTG)	 AG	191519-191673	GC	CGG
(AGC)	 AG	192513-192653	GT	GGG
(AGG)	 AG	192775-192942	GT	AGG
(GCT)	 AG	193123-193263	GT	GGG
(GTG)	 AG	193437-193588	GT	AAG
(GAA)	 AG	193764-194040	CC	CGC
(GCA)	 CG	194071-194104	GT	AGG
(GTG)	 AG	194342-194400	CA	AAC
-recovered CodingQuarry_transcript_32719-T1, initial, 189692, 189906
-recovered CodingQuarry_transcript_32719-T1, terminal, 194342, 194400
-recovered CodingQuarry_transcript_32719-T1, internal, 190193, 190387
-recovered CodingQuarry_transcript_32719-T1, internal, 190570, 190688
-recovered CodingQuarry_transcript_32719-T1, internal, 191519, 191673
-recovered CodingQuarry_transcript_32719-T1, internal, 192513, 192653
-recovered CodingQuarry_transcript_32719-T1, internal, 192775, 192942
-recovered CodingQuarry_transcript_32719-T1, internal, 193123, 193263
-recovered CodingQuarry_transcript_32719-T1, internal, 193437, 193588
Valid prediction for CodingQuarry_transcript_32727-T1
Couldn't classify 81626, 81808
Sorry, prediction pasa_asmbl_28047.p1 fails validation.
(CGC)	 GG	81626-81808	GT	CGG
(GAC)	 AG	81912-82067	GT	AGG
(TCC)	 AG	82234-82326	GT	AGG
(ACA)	 AG	82428-82463	GT	ATG
(ACA)	 AG	82561-82770	AA	AAA
-recovered pasa_asmbl_28047.p1, terminal, 82561, 82770
-recovered pasa_asmbl_28047.p1, internal, 81912, 82067
-recovered pasa_asmbl_28047.p1, internal, 82234, 82326
-recovered pasa_asmbl_28047.p1, internal, 82428, 82463
Valid prediction for GlimmerHMM_glimmerT_48535-T1
Valid prediction for GlimmerHMM_glimmerT_48510-T1
Valid prediction for snap_scaffold_21-snap.2266-T1
Valid prediction for CodingQuarry_transcript_32726-T1
Valid prediction for GlimmerHMM_glimmerT_48519-T1
Valid prediction for GlimmerHMM_glimmerT_48522-T1
Valid prediction for pasa_asmbl_28043.p1
Valid prediction for snap_scaffold_21-snap.2289-T1
Valid prediction for snap_scaffold_21-snap.2293-T1
Valid prediction for snap_scaffold_21-snap.2296-T1
Couldn't classify 179721, 179792
Couldn't classify 180688, 181038
Sorry, prediction pasa_asmbl_28243.p1 fails validation.
(GAG)	 CA	179721-179792	GT	AGG
(TGG)	 AG	180090-180365	GT	AGG
(GTG)	 AG	180688-181038	CG	GTC
-recovered pasa_asmbl_28243.p1, internal, 180090, 180365
Valid prediction for GlimmerHMM_glimmerT_48524-T1
Valid prediction for snap_scaffold_21-snap.2290-T1
Valid prediction for CodingQuarry_transcript_32723-T1
Couldn't classify 65798, 65975
Sorry, prediction pasa_asmbl_28059.p1 fails validation.
(ATG)	 TC	63018-63068	GT	AGG
(AGG)	 AG	63437-63554	GT	ACG
(GTG)	 AG	63640-63770	GT	AGG
(GGT)	 AG	63876-63949	GT	AAG
(CAA)	 AG	64160-64293	GT	AGG
(CAG)	 AG	64873-65029	GT	GTG
(GCT)	 AG	65448-65657	GT	CGG
(GGG)	 AG	65798-65975	GT	AGG
-recovered pasa_asmbl_28059.p1, initial, 63018, 63068
-recovered pasa_asmbl_28059.p1, internal, 63437, 63554
-recovered pasa_asmbl_28059.p1, internal, 63640, 63770
-recovered pasa_asmbl_28059.p1, internal, 63876, 63949
-recovered pasa_asmbl_28059.p1, internal, 64160, 64293
-recovered pasa_asmbl_28059.p1, internal, 64873, 65029
-recovered pasa_asmbl_28059.p1, internal, 65448, 65657
-recovered pasa_asmbl_28059.p1, internal, 65798, 65975
Valid prediction for HiQ_model.g32426.t1
Valid prediction for snap_scaffold_21-snap.2265-T1
Valid prediction for pasa_asmbl_28065.p1
Valid prediction for snap_scaffold_21-snap.2287-T1
Valid prediction for snap_scaffold_21-snap.2291-T1
Couldn't classify 56428, 56489
Sorry, prediction pasa_asmbl_28062.p1 fails validation.
(ATG)	 AA	53691-53693	GT	TGG
(AAC)	 AG	53785-55378	GT	CGG
(GAG)	 AG	56428-56489	GA	CTG
-recovered pasa_asmbl_28062.p1, initial, 53691, 53693
-recovered pasa_asmbl_28062.p1, internal, 53785, 55378
Valid prediction for GlimmerHMM_glimmerT_48530-T1
Valid prediction for GlimmerHMM_glimmerT_48512-T1
Valid prediction for snap_scaffold_21-snap.2278-T1
Valid prediction for snap_scaffold_21-snap.2281-T1
Valid prediction for snap_scaffold_21-snap.2282-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.2298-T1
Valid prediction for Augustus_model.g32421.t1
Valid prediction for Augustus_model.g32408.t1
Couldn't classify 76622, 76792
Couldn't classify 81163, 81284
Sorry, prediction pasa_asmbl_28054.p1 fails validation.
(GTG)	 AG	76622-76792	GT	CGG
(ACC)	 AG	76949-77146	GT	TGG
(GCT)	 AG	77255-78261	GT	CAG
(TCT)	 AG	78387-78564	GT	AGG
(GCC)	 AG	78838-79411	GT	GAG
(ACG)	 AG	79553-80916	GT	CGG
(ATG)	 AG	81001-81070	GT	AGG
(CTC)	 AG	81163-81284	GG	CCG
-recovered pasa_asmbl_28054.p1, initial, 81001, 81070
-recovered pasa_asmbl_28054.p1, internal, 76622, 76792
-recovered pasa_asmbl_28054.p1, internal, 76949, 77146
-recovered pasa_asmbl_28054.p1, internal, 77255, 78261
-recovered pasa_asmbl_28054.p1, internal, 78387, 78564
-recovered pasa_asmbl_28054.p1, internal, 78838, 79411
-recovered pasa_asmbl_28054.p1, internal, 79553, 80916
-recovered pasa_asmbl_28054.p1, internal, 81001, 81070
Valid prediction for Augustus_model.g32420.t1
Valid prediction for CodingQuarry_transcript_32721-T1
Valid prediction for snap_scaffold_21-snap.2302-T1
Valid prediction for snap_scaffold_21-snap.2273-T1
Valid prediction for HiQ_model.g32427.t1
Valid prediction for GlimmerHMM_glimmerT_48511-T1
Valid prediction for pasa_asmbl_28173.p1
Valid prediction for snap_scaffold_21-snap.2286-T1
Valid prediction for snap_scaffold_21-snap.2276-T1
Valid prediction for Augustus_model.g32422.t1
Valid prediction for snap_scaffold_21-snap.2294-T1
Valid prediction for snap_scaffold_21-snap.2263-T1
Valid prediction for Augustus_model.g32416.t1
Valid prediction for GlimmerHMM_glimmerT_48527-T1
Valid prediction for Augustus_model.g32418.t1
Couldn't classify 60921, 61028
Couldn't classify 61609, 61782
Sorry, prediction pasa_asmbl_28060.p1 fails validation.
(GTT)	 GT	60921-61028	GT	AGG
(GTT)	 AG	61273-61416	GT	AGG
(GTG)	 AG	61609-61782	CC	ACC
-recovered pasa_asmbl_28060.p1, internal, 61273, 61416

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7996, rend_intergenic: 7771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10906, rend_intergenic: 8393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12120, rend_intergenic: 11086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34345, rend_intergenic: 18428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34436, rend_intergenic: 34372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39038, rend_intergenic: 34475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42728, rend_intergenic: 40079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59550, rend_intergenic: 53721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81968, rend_intergenic: 61652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96795, rend_intergenic: 87141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106388, rend_intergenic: 98914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115466, rend_intergenic: 114339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139867, rend_intergenic: 137621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167618, rend_intergenic: 162873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176464, rend_intergenic: 171542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186694, rend_intergenic: 184489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202767
-exon list size: 487


building trellis

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75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 7996, rend_intergenic: 7771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10906, rend_intergenic: 8393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12120, rend_intergenic: 11086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34345, rend_intergenic: 18428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34436, rend_intergenic: 34372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39038, rend_intergenic: 34475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42728, rend_intergenic: 40079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59550, rend_intergenic: 53721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81968, rend_intergenic: 61652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96795, rend_intergenic: 87141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106388, rend_intergenic: 98914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115466, rend_intergenic: 114339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139867, rend_intergenic: 137621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167618, rend_intergenic: 162873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176464, rend_intergenic: 171542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186694, rend_intergenic: 184489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support